Why do people take such a big issue with spell banning?

Why do people take such a big issue with spell banning to bring casters in line with other characters? I mean people ban classes, and races and all sorts of other stuff for their games but when I mention spell banning wizards and clerics lose their ****. I dictate what spells are in my game, as well as classes and races, not the players.

I banned shivering touch ahead of time, the PC's didn't complain. Are you giving your PC's enough forewarning that spells are banned? If so, maybe they just need some time to cool off, clerics and wizards are plenty strong, you could rip half the spells out the game and they should still function like small heavily built wreaking balls. Are there any specific spells your banning that cause trouble?

Few things come to mind.
1. Since there are so many (more) spells compared to classes a DM may not be aware of all (understandably), so sometimes it results in retro active ban. If the player had been invested building the character for that spell sometimes levels in advance (similar to players getting miffed if you ban a PrC just as they get ready to take it)
2. Spells are acquired on level up. Often IME players get make their advancement chooses between sessions. Time limitations and all. However, this means that they are already invested in their choice for several days or even more then a week (depending on how often you play). Then they come to the table and puff Denied.
3. For long time players some spells are iconic. Banning "Animate Dead" or Harm can feel like its taking away from the experience. It is like telling them "OK I will run standard 3.X D&D, but no <insert one or more of the PHB classes here>."
4. Tools of the trade feel. PrC are (listed as) optional. Spells are not. Players can feel you are nerfing the class. If a martial class player choose it specifically so s/he can play a longbow archer and the DM said "Mnn, no! Too much range, thrown weapons only." they will be pissed.

Irregardless of the above I am not saying to give in to the players. Just listing some of the clash of assumptions. The DM is (usually) not out to spoil the fun of the other players, but people sometimes take things personally.
As always it is good to sit down with the player and get to the bottom of why exactly are they upset. You should not just give in to their demands, but may end up allowing them to redo some of their previous choices.
For example if they have taken Weapon focus (spell) and you end up banning the "Orb" spells from SC (touch attack roll, save does not reduce damage, no SR), allow them to exchange the feat.

I don't find Break enchantment, Heal, Raise Dead, Stone to Flesh, Limited Wish, Resurrection or Wish/Miracle vital to the game at all. Even detect magic, dispel magic and cure spells are debatable as far as I am concerned.

I've never seen the need to ban spells. If a player was too powerful or too weak, I just adjusted the encounters or gave them a quest heavy on roleplay. Simple as that. Why limit the poor smucks? As long as they only try to beat the monsters and not the game, I couldn't care less for their spell selection in this regard. It's just only natural, after all. If you were to face a dragon, you would use the best means at your disposal to kill the damn thing, so long it's CR's not 4+ below yours. Taking away spells is the D&D equalient of your commander pulling your railgun out of your hand because your opponent(read: the guy who wants to kill you) only has a pistol, and he's sick of your 'unfair advantage'. Not even Knights take honorable battle this far.

Wish and related spells are banned. If you find yourself needing to undo a condition that requires a limited wish or better, its an appeal for direct divine intervention. They aren't on any spell list for mortals to cast.

Raise dead and related spells require an appeal for direct divine intervention. They aren't on any spell list for mortals to cast.

Teleportation spells take you on a barely-shielded trip through the Far Realms. The longer the trip, the more damaging it is to your mental health. They also have a casting time measured in minutes for the longer-ranged versions (anything longer than dimension door).

Divination spells that grant you knowledge through means other than direct observation, such as legend lore (which communicates with an outer being) or comprehend languages (which grants knowledge without perception) are banned. Essentially, the divination school is reduced to those spells that directly enhance your own senses in some way.

Any spell that is keyed off alignment is changed, due to my not using alignment in games. "Detect good" essentially becomes "detect allies of my deity", while "detect evil" becomes "detect enemies of my deity".

Anything that is effectively a "save or die/suck" has a lesser effect over a period of a few rounds, with a save allowed each round. For example, sleep causes fatigue for one round, then exhausted for one round, then sleep (the exhausted condition expires when the spell's original duration expires). Flesh to stone causes 1d6 Con damage per round, with petrifaction occurring when Con reaches 0.

Spells that permanently or "instantaneously" create something from nothing (eg. wall of stone) instead have a duration measured in days or weeks per caster level. Good for an emergency barrier when you need one, but not something you want to be making permanent structures from.

All spells that are listed as taking a standard action or move action to cast instead take a full-round action (some exceptions). Spells that were listed as taking one or more full rounds take an additional full round to cast.

The swift XYZ line of spells take a standard action to cast.

The power word XYX spells take a standard action to cast.

The inflict XYX wounds spells take a standard action to cast.

The cure XYX wounds spells take a standard action to cast. When used to heal, they always heal at least 10% of the target's maximum hp per spell level, regardless of the die roll.

So while I haven't specifically named most of the spells affected, players do know what to expect.

* Any spell that is keyed off alignment is changed, due to my not using alignment in games. "Detect good" essentially becomes "detect followers of my deity", while "detect evil" becomes "detect enemies of my deity".

Interesting. I haven't ever played a campaign without Alignment rules. I can see the appeal of it, but does it work out? Let's say there is an Evil deity who's allied with demons at large due to the portfolio. And a demon wants to kill a worshipper because, well, it's a demon; depending on how dump it is, it might murder him on a just 'cause basis. Wouldn't that trigger a bell for our hypothetical worshipper, given enough time before said demon chops his head off?